Systems Biological Applications for Fungal Gene Expression

  • Gunseli Bayram Akcapinar
  • Osman Ugur Sezerman
Part of the Fungal Biology book series (FUNGBIO)


Recent advancements in omics technologies are instrumental in studying to molecular events and to reveal the underlying mechanisms. In this chapter we focus on use of different types of omics data to understand the fungal gene expression and translation mechanism. These data were analyzed in a system biology approach providing valuable insights for efficient use of fungal expression systems to achieve high production yields.


Fungi Transcriptomics Metabolomics Secretome Proteome Glycosylation Transcription regulation 


  1. Brandl J, Andersen MR. Current state of genome-scale modeling in filamentous fungi. Biotechnol Lett. 2015;37:1131–9. doi: 10.1007/s10529-015-1782-8.CrossRefGoogle Scholar
  2. Cesbron F, Oehler M, Ha N, et al. Transcriptional refractoriness is dependent on core promoter architecture. Nat Commun. 2015;6:6753. doi: 10.1038/ncomms7753.CrossRefGoogle Scholar
  3. Cregg JM, Cereghino JL, Shi J, Higgins DR. Recombinant protein expression in Pichia pastoris. Mol Biotechnol. 2000;16:23–52. doi: 10.1385/MB:16:1:23.CrossRefGoogle Scholar
  4. Deshpande N, Wilkins MR, Packer N, Nevalainen H. Protein glycosylation pathways in filamentous fungi. Glycobiology. 2008;18:626–37. doi: 10.1093/glycob/cwn044.CrossRefGoogle Scholar
  5. Dreyfuss JM, Zucker JD, Hood HM, et al. Reconstruction and validation of a genome-scale metabolic model for the filamentous fungus Neurospora crassa using FARM. PLoS Comput Biol. 2013;9:e1003126. doi: 10.1371/journal.pcbi.1003126.CrossRefGoogle Scholar
  6. Dvir S, Velten L, Sharon E, et al. Deciphering the rules by which 5′-UTR sequences affect protein expression in yeast. Proc Natl Acad Sci. 2013;110:E2792–801.CrossRefGoogle Scholar
  7. Häkkinen M, Arvas M, Oja M, et al. Re-annotation of the CAZy genes of Trichoderma reeseiand transcription in the presence of lignocellulosic substrates. Microb Cell Factories. 2012;11:134. doi: 10.1186/1475-2859-11-134.CrossRefGoogle Scholar
  8. Horta MAC, Vicentini R, Delabona P d S, et al. Transcriptome profile of Trichoderma harzianum IOC-3844 induced by sugarcane bagasse. PLoS One. 2014;9:e88689. doi: 10.1371/journal.pone.0088689.CrossRefGoogle Scholar
  9. Kitano H (2002) Systems Biology: A Brief Overview. Science 295:1662–1664.Google Scholar
  10. Kolbusz MA, Di Falco M, Ishmael N, et al. Transcriptome and exoproteome analysis of utilization of plant-derived biomass by myceliophthora thermophila. Fungal Genet Biol. 2014;72:10–20. doi: 10.1016/j.fgb.2014.05.006.
  11. Liu G, Zhang L, Qin Y, et al. Long-term strain improvements accumulate mutations in regulatory elements responsible for hyper-production of cellulolytic enzymes. Sci Rep. 2013;3:1569. doi: 10.1038/srep01569.Google Scholar
  12. Liu L, Feizi A, Österlund T, et al. Genome-scale analysis of the high-efficient protein secretion system of Aspergillus oryzae. BMC Syst Biol. 2014;8:73.CrossRefGoogle Scholar
  13. Mattanovich D, Branduardi P, Dato L, et al. Recombinant protein production in yeasts. Methods Mol Biol (Clifton NJ). 2012;824:329–58. doi: 10.1007/978-1-61779-433-9_17.CrossRefGoogle Scholar
  14. Miao Y, Liu D, Li G, et al. Genome-wide transcriptomic analysis of a superior biomass-degrading strain of A. fumigatus revealed active lignocellulose-degrading genes. BMC Genomics. 2015;16:459. doi: 10.1186/s12864-015-1658-2.CrossRefGoogle Scholar
  15. Nevalainen H, Peterson R. Making recombinant proteins in filamentous fungi-are we expecting too much? Front Microbiol. 2014;5:75.Google Scholar
  16. Pitkänen E, Jouhten P, Hou J, et al. Comparative genome-scale reconstruction of gapless metabolic networks for present and ancestral species. PLoS Comput Biol. 2014;10:e1003465. doi: 10.1371/journal.pcbi.1003465.CrossRefGoogle Scholar
  17. Puxbaum V, Mattanovich D, Gasser B. Quo vadis? The challenges of recombinant protein folding and secretion in Pichia pastoris. Appl Microbiol Biotechnol. 2015;99:2925–38. doi: 10.1007/s00253-015-6470-z.CrossRefGoogle Scholar
  18. Su X, Schmitz G, Zhang M, et al. Heterologous gene expression in filamentous fungi. Adv Appl Microbiol. 2012;81:1–61. doi: 10.1016/B978-0-12-394382-8.00001-0.CrossRefGoogle Scholar
  19. Tan K-C, Ipcho SVS, Trengove RD, et al. Assessing the impact of transcriptomics, proteomics and metabolomics on fungal phytopathology. Mol Plant Pathol. 2009;10:703–15. doi: 10.1111/j.1364-3703.2009.00565.x.CrossRefGoogle Scholar
  20. Van Munster JM, Nitsche BM, Akeroyd M, et al. Systems approaches to predict the functions of glycoside hydrolases during the life cycle of Aspergillus niger using developmental mutants ∆brlA and ∆flbA. PLoS One. 2015;10:e0116269. doi: 10.1371/journal.pone.0116269.CrossRefGoogle Scholar
  21. Vongsangnak W, Ruenwai R, Tang X, et al. Genome-scale analysis of the metabolic networks of oleaginous Zygomycete fungi. Gene. 2013;521:180–90. doi: 10.1016/j.gene.2013.03.012.CrossRefGoogle Scholar
  22. Xiong Y, Coradetti ST, Li X, et al. The proteome and phosphoproteome of Neurospora crassa in response to cellulose, sucrose and carbon starvation. Fungal Genet Biol. 2014;72:21–33. doi: 10.1016/j.fgb.2014.05.005.CrossRefGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Gunseli Bayram Akcapinar
    • 1
  • Osman Ugur Sezerman
    • 2
  1. 1.Microbiology Group, Research Area Biotechnology and MicrobiologyInstitute of Chemical Engineering, Vienna University of TechnologyViennaAustria
  2. 2.Department of Biostatistics and Medical InformaticsAcibadem UniversityIstanbulTurkey

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